Sub-micron polycrystalline diamond films deposited using H2/CH4 gasses show Raman peaks at ~1130 and ~1470, which have been assigned to the ν1 and ν3 modes of t-PA hydrocarbons within the diamond intergranular space. Here we report the isotopic shift of these peaks in similar diamond films grown from D2/CD4 gas mixtures, as well as the splitting of the 1130cm−1 peak to two peaks at 880 and 855cm−1. We suggest that this unexpected peak splitting is due to an excess of short conjugated t-PA chains and relate this to the lower amount of amorphous carbon in these deuterated films, as evidenced by Raman spectroscopy and secondary ion mass spectrometry (SIMS). This difference in grain boundary amorphous carbon content is also suggested to explain a measured difference in thermal out-diffusion of deuterium from these films, as compared to hydrogen in standard films. A third unreported Raman peak at 820cm−1 is also examined and shown to be related to stressed SiC, seen to relax during high temperature vacuum annealing. The reduction of observed stress is partly assigned to an increase of the sp3/sp2 ratio in the film after annealing.